Creates a new sequence by adding markers.
Simulated data from a backcross population
OneMap interface with MDSMap package with possibilitie of multipoint distances estimation
Read data from a Mapmaker raw file
test_segregation
Assign markers to preexisting linkage groups
test_segregation_of_a_marker
test_segregation_of_a_marker
Mapping functions Haldane and Kosambi
Construct the linkage map for a sequence of markers
Informs the segregation patterns of markers
Search for the best order of markers combining compare and try_seq
functions
Internal onemap functions
Read data from all types of progenies supported by OneMap
Data generated from VCF file with biallelic markers from a f2 intercross population
Draw a graphic of raw data for any OneMap population
Show the results of segregation tests
Print method for object class 'rf_2pts'
Show markers with/without segregation distortion
Create a sequence of markers
Simulated data from a backcross population
Convert vcfR object to onemap object
Suggests a LOD Score for two point tests
Simulated data from a RIL population produced by selfing.
Recombination Counting and Ordering
Defines the default mapping function
Data generated from VCF file with biallelic markers from a full-sib family derived from two outbred parents
Draw a graphic showing the number of markers of each segregation pattern.
Plot p-values for chi-square tests of expected segregation
Two-point analysis between genetic markers
Convert variants from a VCF file to OneMap file format
Seriation
Simulated data from a F2 population
Assign markers to linkage groups
Allocate markers into bins
Show the results of grouping procedure
Data generated from VCF file with biallelic markers from a f2 backcross population
Show the results of grouping markers to preexisting sequence
Plots pairwise recombination fractions and LOD Scores in a heatmap
Compares and displays plausible alternative orders for a given linkage
group
Rapid Chain Delineation
Data from a full-sib family derived from two outbred parents
Data generated from VCF file with biallelic markers from a RIL population produced by selfing
Simulated data from a F2 population
Try to map a marker into every possible position between markers
in a given map
Unidirectional Growth
Print method for object class 'try'
Convert onemap object to onemap raw file
Write a genetic map to a file
New dataset based on bins
Calculates individual significance level to be used to achieve a global alpha (with Bonferroni)
Creates a new sequence by dropping markers.
Draw a linkage map
Combine OneMap datasets
Draw a genetic map
C++ routine for multipoint analysis in outcrossing populations
Compare all possible orders (exhaustive search) for a given sequence of
markers
create_dataframe_for_plot_outcross
Create a dataframe suitable for a ggplot2 graphic